Self assembled nano-devices using DNA

ABSTRACT

An article of manufacture including an organic structure and inorganic atoms bonded to specific locations on the organic structure.

REFERENCE TO RELATED APPLICATION

This is a continuation of application Ser. No. 09/604,680, filed Jun.27, 2000, now abandoned, which is a continuation of Ser. No. 09/154,575,filed Sep. 17, 1998, now abandoned.

FIELD OF THE INVENTION

The present invention relates to the field of semiconductor chips. Inparticular, the present invention relates to semiconductor chips thatinclude active device having extremely small feature sizes. The presentinvention also relates to methods for forming semiconductor chipsincluding active features having such sizes.

BACKGROUND OF THE INVENTION

The shrinking dimensions of active devices on silicon chip isapproaching its limit due to restrictions set by photolithographictechniques. For example, wave properties of radiation, such asinterference and diffraction, can limit device size and density.Considerable research has taken place to overcome the limitations ofphotolithographic techniques.

The research has been directed at correcting the problems, such as byphase shift lithography as well as to developing other novel approaches.Concomitantly, with this research, there have been developments indevice design utilizing electron confinement in small volume. The threebasic categories are such devices design are Quantum Dots (QD), ResonantTunneling Devices (RTD), and Single Electron Transistors (SET). QuantumDots are discussed in greater detail in R. Turton, The Quantum Dot,Oxford, U.K., Oxford University Press, 1995; Resonant Tunneling Devicesare discussed in greater detail in A. C. Seabaugh et al., FutureElectron Devices (FED) J., Vol. 3, Suppl. 1, pp. 9-20, (1993); andSingle Electron Transistors are discussed in greater detail in M. A.Kastner, Rev. Mod. Phys., Vol. 64, pp. 849-858, (1992); the entiredisclosures of all of which is hereby incorporated by reference.

SUMMARY OF THE INVENTION

Aspects of the present invention provide an article of manufactureincluding an organic structure and inorganic atoms bonded to specificlocations on the organic structure.

Other aspects of the present invention includes a structure including aDNA molecule that includes an R-loop. A nanoparticle is bound to the DNAmolecule in the interior of the R-loop.

Additional aspects of the present invention provide a structure thatincludes an electrode positioned by a biomolecule and a nanoparticlespaced apart from the biomolecule.

Further aspects of the present invention provide a method for selfassembly of inorganic material utilizing a self assembled organictemplate. The method includes forming an organic structure and bondinginorganic atoms to specific locations on the organic structure.

Still further aspects of the present invention provide a structureincluding a substrate, a first electrode and a second electrode on thesubstrate, and an organic molecule extending between the first electrodeand the second electrode. A nanoparticle bonded to the organic molecule.

Also, aspects of the present invention provide a method for forming astructure. The method includes forming a first electrode on a substrate.A second electrode is formed on the substrate. A DNA molecule isextended between the first electrode and the second electrode. At leastone nanoparticle is inserted into at least one location in the DNAmolecule.

Still other objects and advantages of the present invention will becomereadily apparent by those skilled in the art from the following detaileddescription, wherein it is shown and described only the preferredembodiments of the invention, simply by way of illustration of the bestmode contemplated of carrying out the invention. As will be realized,the invention is capable of other and different embodiments, and itsseveral details are capable of modifications in various obviousrespects, without departing from the invention. Accordingly, thedrawings and description are to be regarded as illustrative in natureand not as restrictive.

BRIEF DESCRIPTION OF THE DRAWINGS

The above-mentioned objects and advantages of the present invention willbe more clearly understood when considered in conjunction with theaccompanying drawings, in which:

FIGS. 1a, 1 e, and 1 f represent overhead views and FIGS. 1b, 1 c, and 1d represent cross-sectional views of an embodiment of a device accordingto the present invention at various stages of an embodiment of a processaccording to the present invention;

FIG. 2 represents a cross-sectional view of a device illustrated in FIG.1a;

FIG. 3 represents an embodiment of an embodiment of a DNA molecule thatmay be utilized according to the present invention;

FIG. 4 represents an embodiment of a nanoparticle that may be utilizedaccording to the present invention;

FIG. 5 represents an embodiment of an embodiment of a DNA moleculeincluding an R-loop and an embodiment of a nanoparticle that may beutilized according to an embodiment of the present invention;

FIG. 6 represents an overhead view of an embodiment of a deviceaccording to the present invention;

FIG. 7 represents a cross-sectional view of the embodiment of a deviceillustrated in FIG. 6;

FIG. 8 represents an overhead view of an embodiment of a deviceaccording to the present invention that forms an AND gate; and

FIG. 9 represents an overhead view of an embodiment of a deviceaccording to the present invention that forms an OR gate.

DETAILED DESCRIPTION OF THE INVENTION

The present invention provides methods for overcoming and actuallycircumventing problems associated with photolithographic techniques. Theresulting devices are potentially much smaller than those created by thecommonly known techniques. Accordingly, the present invention includes anovel fabrication method to make devices on a nanometer scale, ornanodevices. The present invention could be considered to fall under thecategory of a Resonant Tunneling Device referred to above.

To create such devices, the present invention utilizes theself-organizational nature of some biological molecules. For example,the present invention may make use of nucleic acids and theirproperties, including their self-organizational nature. In particular,the present invention may utilize both deoxyribonucleic acid (DNA) andribonucleic acid (RNA) to create the devices.

The nature of DNA and RNA is well known. A few nucleic acid bases areattached together to make up a longer molecule. In the case of DNA, twoof these longer molecules are bonded together and form a double helixstructure. RNA molecules typically are formed by transcribing one strandof the double stranded DNA during protein synthesis. For backgroundpurposes, reference is made to BIOCHEMISTRY, Lubert Stryer, W.H. Freemanand Company, the entire contents of which are hereby incorporated byreference.

A structure according to the present invention typically includes asubstrate upon which the nanodevices of the invention may be createdupon. The substrate may include a glass. Also, the substrate, whether aglass other form, may include any common semiconductor material. Forexample, the substrate may include silicon.

Electrodes may be arranged on the substrate. Typically, at least twoelectrodes are arranged on the substrate. The electrodes may be formedon the substrate according to common photolithographic techniques.

The electrodes may be made of any oxide free, electrically conductingmaterial. For example, the electrodes may be made of any noble metal oralloy that includes noble metal. Preferably, the electrodes are made ofan oxide-free metal. According to one example, the electrodes are madeof gold.

FIG. 1a represents an overhead view of an embodiment of a substrate 1with two electrodes, a first electrode 3 and a second electrode 5,provided on the surface of the substrate or on other structures formedin and/or on the substrate. The first electrode 3 and second electrode 5may be provided in close proximity to each other. The distance betweenthe first electrode and the second electrode may vary, depending uponthe embodiment. According to one example, the first electrode and thesecond electrode may be separated by a distance of from about 0.1 μm toabout 100 μm. Typically, the electrodes are separated by a distance offrom about 1 μm to about 10 μm. Additionally, the electrodes typicallyhave a thickness of about 20 nm to about 1000 nm.

The first electrode and the second electrode may have a variety ofshapes, depending upon the embodiment. FIG. 1(a) illustrates an examplein which the first electrode 3 and the second electrode 5 terminate inpoints 7 and 9 that face each other. Although the sides of the electrodethat 2, 4, 6, and 8 that form the points are curved in the embodimentshown in FIG. 1(a), the sides may have any curve, including straight.The configuration of the remaining portion of the first electrode andthe second electrode may vary, as long as the remaining portion providesan area for connection of a power source to apply power to the firstelectrode and the second electrode.

The present invention may include a third electrode 11 on the substrate1. The third electrode 11 may be referred to as a gate electrode. Thefunction of the third electrode will be discussed below in greaterdetail.

The third electrode 11 may be positioned between the first electrode 3and the second electrode 5 as illustrated in the embodiment shown inFIG. 1(a). The third electrode 11 may also be formed by utilizing commonphotolithographic techniques, although other techniques may be utilized.

The configuration, such as the shape, of the third electrode 11 mayvary, depending upon the embodiment. For example, the third electrode 11illustrated in FIG. 1(a) is substantially a long, thin rectangle, inother words, substantially a straight line.

The thickness of the third electrode may vary, depending upon theapplication. For example, the third electrode may have a width of fromabout 100 nm to about 5000 nm. Preferably, the third electrode is asthin as possible. According to one embodiment, the third electrode has athickness of less than about 100 nm.

The dimensions, especially the thickness, of the three electrodes,including the third electrode may be controlled by a variety of factors.For example, the dimensions of the electrodes, and especially the thirdelectrode, may be controlled by the quality of the film, such as thenoble metal or alloy described above, that the electrodes are made of.Film quality characteristics that may affect dimensions of the thirdelectrode include smoothness, conductivity and adhesion.

The exact location of the third electrode may vary, depending upon theembodiment. For example, the purpose of the third electrode may controlits position. According to one embodiment, the third electrode 11 ispositioned equidistant from the tips 7 and 9 of the first electrode 3and the second electrode 5. According to one embodiment, the thirdelectrode may be arranged such that it is perpendicular to a lineconnecting the points 7 and 9 of the first electrode 3 and the secondelectrode 5.

As with the first electrode 3 and the second electrode 5, the thirdelectrode 11 may be made of any electrically conducting material. Forexample, the third electrode may be made of any metal, or alloy.Preferably, the third electrode is made of an oxide-free metal.According to one example, the third electrode is made of gold.

FIG. 2 represents a cross-sectional view of the embodiment of thesubstrate and the first electrode, the second electrode, and the thirdelectrode shown in FIG. 1a.

The present invention may also include a fourth electrode positionedbetween the first electrode 3 and the second electrode 5. FIG. 8illustrates such an embodiment. The fourth electrode may besubstantially similar to the third electrode described above. Accordingto some embodiments, more than one electrode may extend between eachpair of electrodes.

Additionally, the present invention may include more than one pair ofelectrodes such as the first electrode 3 and the second electrode 5. Forexample, the embodiment of the device illustrated in FIG. 9 includes twopairs of electrodes. Each pair of electrodes in the embodiment shown inFIG. 9 includes an electrode therebetween similar to the electrode 11between the first electrode 3 and the second electrode 5 in theembodiment shown in FIG. 1a.

After provision of the electrodes, whether by photolithographictechniques or otherwise, at least one organic structure may be extendedbetween the first electrode 3 and the second electrode 5, as in theembodiment illustrated in FIG. 1a. However, it is not necessary that theorganic structure extend between two electrodes. The at least oneorganic structure may include at least one inorganic atom bonded to atleast one specific location. The bonding could be any sort of bonding,whether hydrogen, ionic, covalent or otherwise. The inorganic atoms maybe electrically conducting and form an electrical conductor.

The at least one inorganic atom that may be bonded to the organicstructure could include a nanoparticle. The nanoparticle may include atleast one partially electrically conducting material. For example, thenanoparticle may include at least one material selected from the groupconsisting of a noble metal or a noble metal alloy. According to oneexample, the nanoparticle is gold.

The nanoparticle can include a plurality of elements. For example, ifthe nanoparticle is gold, the gold may be in a ball having a diameter offrom about 1 nm to about 100 nm. The particle may be coated with atleast one surfactant. The surfactant may have terminal groups x and y.The groups x and y may be arranged at the end of a polymer. For example,the groups x and y may be bonded to the ends of a polymer. The polymermay include a variety of monomers. Examples of the monomers include

CH₂_(n), CH₂—O_(n), and

wherein n>1; R and R′=CH₃, C₂H₅,

The group x may include —SH. On the other hand, the group y may include

or a nucleotide base.

The x group may bond with the gold or silver, for example, particle. They group may bond with the nucleotide. If y is an acid group, the acidgroup may react wit the amine group of the DNA base. If y is anucleotide base group, the base may hydrogen bond to the DNA molecule.

As stated above, the present invention includes an organic structure.The organic structure may extend between the first electrode 3 and thesecond electrode 5 as discussed above. The organic structure may includeDNA.

The DNA that may be included in the present invention may be singlestranded or double stranded. The length of the DNA strand included inthe organic structure according to the present invention may be fromabout 300 to about 300,000 bases, or base pairs in the case of doublestranded DNA. Alternatively, the length of the DNA molecule may be about0.1 μm to about 100 μm.

According to one embodiment, the DNA is λ-DNA. However, any DNA moleculehaving any sequence of bases may be utilized according to the presentinvention. In other words, the DNA may be subjectively selected.

The DNA molecule that may be included in a structure according to thepresent invention may include an R-loop. Description of R-loops may befound in Asai and Kogoma, D-Loops and R-Loops: Alternative Mechanismsfor the Initiation of Chromosome Replication in Escherichia coli,JOURNAL OF BACTERIOLOGY, April 1994, pp. 1807-1812; Landgraf et al.,R-loop stability as a function of RNA structure and size, NUCLEIC ACIDSRESEARCH, 1995, Vol 23, No. 7, pp. 3516-3523; Landgraf et al., Doublestranded scission of DNA directed through sequence-specific R-loopformation, NUCLEIC ACIDS RESEARCH, 1995, Vol 23, No. 7, pp. 3524-3530;and Masai and Arai, Mechanisms of primer RNA synthesis andD-loop/-R-loop dependent DNA replication in Escherichia coli, BIOCHEMIE(1996) 78, pp. 1109-1117, the entire contents of all of which are herebyincorporated by reference.

The R-loop may function to provide a site for the attachment of thenanoparticle(s) to the DNA molecule. Accordingly, the DNA molecule mayinclude at least one R-loop. FIG. 9 illustrates an embodiment thatincludes two R-loops.

Each R-loop may include at least one nanoparticle bonded to a portion ofthe DNA within the R-loop. In addition to including more than oneR-loop, more than one nanoparticle could be attached to a portion of theDNA molecule within each R-loop. Steps for attaching the nanoparticle(s)to the R-loop are discussed below in greater detail.

The R-loops may be formed according to any known technique for formingR-loops, such as those disclosed in the above-references scientificliterature articles. At least one RNA molecule having a sequencecomplementary to at least one portion of the DNA molecule may beutilized in formation of the R-loop. As stated above, the DNA moleculemay include more than one R-loop. Therefore, the more than one RNAmolecule may be utilized to form R-loops in the DNA molecule. Each RNAmolecule may have a sequence complementary to a different sequence ofthe DNA molecule.

The sequence of the RNA molecule may be controlled to control where theR-loop(s) is(are) created. For example, if the DNA molecule is toinclude one R-loop and the R-loop is to be centrally located in the DNAmolecule, the RNA molecule may have a sequence complementary to asequence of the DNA molecule such that the RNA molecule will besubstantially centered on the DNA molecule, equidistant from the ends ofthe DNA molecule upon formation of the R-loop. According to anotherexample, such as that shown in FIG. 9, the RNA molecules may have asequence complementary to sequences of the DNA molecule such that theRNA molecules will be positioned to divide the DNA molecule into threeportions having substantially equal lengths upon formation of theR-loop.

The sequence of the RNA molecule that may be utilized in forming theR-loop(s) may vary, depending upon the positioning of the DNA moleculerelative to an electrode that may lie under the DNA molecule. Alongthese lines, the RNA molecule may have a sequence such that the R-loopmay be positioned over an underlying electrode. If the present inventionincludes more than one R-loop and the R-loops each overly an electrode,the RNA molecules utilized in forming the R-loops may have sequencessuch that the R-loops will be positioned over the underlying electrodes,such as the third electrode 11 in the embodiment illustrated in FIG. 1a.

As stated above, the present invention may include at least onenanoparticle. To facilitate bonding of the nanoparticle to the organicstructure, the nanoparticle may include one or more atoms or chemicalgroups attached to the nanoparticle. By attaching one or more such atomsor groups, the nanoparticle may be “functionalized”.

In the case where the organic structure includes a DNA molecule, atleast one nucleotide may be attached to the nanoparticle. The at leastone nucleotide attached to the nanoparticle typically is complementaryto at least one nucleotide within the R-loop of the DNA molecule on theportion of the R-loop not attached to the RNA molecule. Therefore, thenucleotide attached to the nanoparticle may depend upon the sequence ofthe DNA molecule and where it is desired that the nanoparticle attach tothe DNA molecule. The nanoparticle and the attachment of thenanoparticle to the DNA molecule are discussed above in greater detail.

The nanoparticle may attach to the portion of the DNA molecule anywherewithin the R-loop. According to one embodiment, the nanoparticleattaches to the DNA about in the center of the portion that lies withinthe R-loop. Therefore, the location of the R-loop may depend upon thelocation of the R-loop. For example, the nanoparticle may be attached tothe DNA molecule midway between the ends of the DNA molecule if the DNAmolecule includes one R-loop substantially in the center of the DNAmolecule.

The present invention may include an electrically conducting material onthe organic structure. The electrically conducting material may includeany electrically conducting material. According to one example, silvermay form a salt with the organic structure. Metallic silver may also beprovided on the organic structure.

The electrically conducting material on the organic structure provides aconductor on the organic structure. In certain cases, this conductor maybe used to form functional structures. An electrically conductingmaterial on the organic structure may provide a capacitive linkagebetween the electrically conducting material on the organic structureand an underlying electrode. This may be accomplished through thefunctionalizing atoms and/or groups of atoms on the nanoparticle. Theconductor (s) on the organic structure may be utilized in forming logicdevices. For example, as described below in greater detail, a structureaccording to the present invention may be utilized in forming an ANDgate and an OR gate, among other structures.

In the case where the organic structure includes DNA, an R-loop in theDNA and a nanoparticle attached to the DNA molecule in the R-loop, theelectrically conducting material on the organic structure may provide aconductor to the two sides of the R-loop on the DNA molecule.

The electrically conducting coating may be applied to the organicstructure by immersing the organic structure in a solution that includessilver ions. The silver ions in the solution may then form a silver saltwith the organic structure. In the case where the organic structureincludes DNA, the silver may form a salt with phosphate groups of theDNA molecule.

After formation of a salt, the silver in the salt may be reduced tometallic silver with a reducing agent. Examples of reducing agents thatmay be utilized include hydroquinone/OH⁻ followed by hydroquinone/OH⁺.

The organic structure may be connected to electrodes on the surface of asubstrate, such as the first electrode and the second electrode in theembodiment illustrated in FIG. 1a. The electrodes are described above ingreater detail. The connection may be effected in a variety of ways. Forexample, the connection may be carried out by providing sites on theelectrodes that the organic structure may be attached to.

The attachment sites may be provided by a variety of structure. Forexample, one or more atoms or molecules may be provided on one or moreof the electrodes. According to one example, at least one organicmolecule is provided on at least one of the electrodes. The organicmolecule could be bonded to the surface of the electrode(s).

According to one example, in which the organic structure includes a DNAmolecule extending between the first electrode and the second electrode,at least one DNA and/or RNA molecule may be attached to the firstelectrode 3 and the second electrode 5 shown in FIG. 1A. In the casewhere the organic structure includes DNA, typically, DNA is provided onthe first electrode and the second electrode. The DNA may be provided onthe electrodes in a variety of ways.

According to one example, the DNA is bonded to an atom or molecule thatfacilitates its connection to the electrodes. For example, the DNA couldbe sulfur terminated. The sulfur terminated ends could attach to thesurface of the gold electrodes. It is well known that S⁻ terminatedcompounds bond to a gold surface.

The DNA molecule extending between the first electrode and the secondelectrode may bond to the DNA and/or RNA on the electrodes. For example,both the DNA molecule that is to extend between the two electrodes andthe DNA molecule(s), as in the above example, attached to the electrodescould have a single stranded portion. The single stranded portions onthe DNA molecule that is to extend between the first electrode and thesecond electrode and the DNA molecule(s) attached to the first electrodeand the second electrode may have complementary ends to facilitate theirbonding to each other.

According to one embodiment, the DNA that is attached to the electrodesis single stranded, sulfur terminated DNA. Regardless of whether singleor double stranded DNA or RNA is bonded to the electrodes, the DNAand/or RNA may include from about 5 to about 20 bases. However, the DNAand/or RNA molecules could be as long as about 100 bases. For example,the DNA and/or RNA molecules could be about 15 to about 30 bases.However, the DNA and/or may be as short or as long as necessary toensure that the DNA and/or functions to attach to the first electrodeand the second electrode the DNA and/or that is to extend between thefirst electrode and the second electrode.

Additionally, regardless of whether single or double stranded DNA or RNAmolecules are bonded to the electrodes, the DNA and/or RNA moleculesattached to one electrode may have a different sequence of bases thanthe DNA and/or RNA molecules attached to the other of the electrodes.Alternatively, a portion of the DNA and/or RNA molecules that the DNAthat is to extend between the first electrode and the second electrodemay have a different sequence, rather than the entire DNA and/or RNAmolecules.

According to an embodiment in which DNA molecules are attached to theelectrodes and the DNA molecules include a sequence of bases to bond tothe DNA molecule that is to extend from between the first electrode andthe second electrode, the DNA molecule that is to extend between thefirst electrode and the second electrode may include “sticky ends” thathave a sequence of bases that is complementary to the DNA attached tothe first electrode and the second electrode.

FIG. 3 illustrates an embodiment of a DNA molecule 21 that is to extendbetween the first electrode and the second electrode. The DNA molecule21 is shown in a linear configuration. The sticky ends 23 and 25 areprovided on the ends of the DNA molecule.

After constructing or otherwise obtaining the DNA molecules to beattached to the first electrode and the second electrode they may beattached to the electrodes. A solution may be formed, that the DNAmolecules are to be added to. First, an aqueous solution of a salt isformed. One Example of a salt is sodium chloride. Each DNA molecule,where a different molecule is to be attached to each electrode, may thenbe added to the solutions.

After formation of the solutions, a quantity 13 of one solution may beplaced on the first electrode 3 and a quantity 15 of the other solutionmay be placed on the second electrode 5. Which solution is placed onwhich electrode may depend upon how it is desired that the DNA moleculethat is to extend between the first electrode and the second electrodeis to be oriented. The quantity of the solution deposited on eachelectrode may depend upon the concentration of the DNA, RNA, and/orother molecule that is in the solutions.

In determining the above factors, the resulting final structure isimportant. That is, one DNA bridge from electrode 3 to electrode 5should form. The concentration of volume typically is secondary. Aflowing solution could also be utilized.

After application of solutions to the first electrode and the secondelectrode to deposit the desired molecules on the electrodes, thesolutions may be removed. Typically, the solutions are permitted toremain on the electrodes for a time sufficient for a number of moleculeto be attached to the electrodes to facilitate the attachment of theorganic structure between the two electrodes. Typically, the solutionsremain for a time of about 10 minutes to about 20 minutes.

Removal of the solution may be carried out in a number of ways. Forexample, the solution may be washed off. For example, water could beutilized to wash the solution off. Typically, the solution is washed offwith a liquid that does not include any moieties that attach to —S—Aubonds. Alternatively, the solution could be permitted to dry with ourwithout the application of heat. According to one example, an air guncould be utilized.

FIG. 1c illustrates the first electrode 3 and the second electrode 5once the solution has been removed. The molecules 17 and 19 remainattached to the first electrode and the second electrode.

After attachment of the anchoring molecules to the electrodes, thestructure that is to extend between the first electrode and the secondelectrode may be applied to the structure, such as illustrated in FIG.1c. In the case where the organic structure includes DNA, the DNA may beapplied to the substrate over the electrodes and space between theelectrodes. The organic structure could be applied in a solution. Onemethod for creating a DNA bridge between electrodes is disclosed inBraun et al., DNA-templated assembly and electrode attachment of aconducting silver wire, Nature, Vol. 391, pp.775-777, Feb. 19, 1998, theentire contents of which is hereby incorporated by reference.

After application of the DNA molecule(s), the ones that are to extendbetween the first electrode and the second electrode, to the substrateand electrodes they may bond to an organic structure, such as anchoringmolecules, attached to the electrodes. To promote a desired orientationof the DNA molecules with respect to the electrodes and anchoringmolecules, such as the DNA described above, the DNA that is to extendbetween the first electrode and the second electrode may be subjected toconditions that tend to align them. The conditions could includesubjecting the DNA molecules to an E-field or a flow field. If anE-field is utilized, it may be from about 10⁴ to about 10⁶ V/cm. On theother hand, if a flow field is utilized, V may be from about 1 to about100 cm/sec.

Encouraging the DNA to align in a particular manner helps to ensure thatat least one of the DNA molecules will extend between the firstelectrode and the second electrode. Typically, how only “DNA bridge” isformed between the electrodes. Additionally, typically, no DNA bridgeswill extend outside of the region where the DNA bridge is shown in FIG.1d.

To facilitate formation of the DNA bridge(s), a fluorescent dye may beutilized to tag the DNA. The experiment is done under a microscope. Assoon as one bridge is formed, the solution containing the DNA may bepurged from the area of the electrodes.

After bonding of the DNA molecule(s) to the first electrode and thesecond electrode, at least one R-loop may be formed in each DNA moleculethat forms a “bridge” between the first electrode and the secondelectrode. Typically, the R-loop is formed in a region of the DNAmolecules between the first electrode and the second electrode that isarranged over another electrode, such as the third electrode describedabove. The formation of the R-loop is described above. FIG. 1eillustrates a DNA molecule 21 extending between the first electrode andthe second electrode, wherein the DNA molecule includes one R-loop 27 inthe region of the DNA molecule over the third electrode 11.

After formation of the R-loop(s), a nanoparticle 29 may be bonded to theDNA molecule. The nanoparticle may be bonded to a portion of the DNAmolecule that lies within the R-loop and is not attached to the RNAmolecule. To accomplish attachment of the nanoparticle to the DNAmolecule, a suspension of the nanoparticle may be formed. The suspensionmay include nanoparticles with a modified surface, as described above.The nanoparticles may be suspended in water at a concentration of about0.1% to about 10%.

After formation of the solution it may be dispensed in a region over theR-loop. The “functionalizing” nucleotides 31 and/or atoms and/ormolecules attached to the nanoparticle 29 may then bond to the DNAwithin the R-loop. FIG. 4 illustrates a nanoparticle 29 with attachednucleotides 31. In the embodiment illustrated in FIG. 4, fournucleotides are attached to the nanoparticle. Typically, about 1 toabout 10000 nucleotides attach to the nanoparticle. The nucleotide(s)attached to the nanoparticle may be complementary to one or morenucleotides within the R-loop as described in greater detail above.

In the case of nucleotides on a nanoparticle bonding to a DNA molecule,the nucleotides on the nanoparticle may hydrogen bond to the nucleotidesof the DNA molecule(s).

FIG. 1f illustrates a DNA molecule extending between a first electrode 3and a second electrode 5, wherein the DNA molecule includes one R-loopwith one nanoparticle bonded to the DNA molecule within the R-loop. FIG.5 illustrates a close-up view of an embodiment of the DNA molecule, inits double helix configuration, with the R-loop 27, attached RNA 33,nanoparticle 29, and nucleotides 31 attached to the nanoparticle.

After attachment of the nanoparticle(s) to the DNA molecule extendingbetween the first electrode and the second electrode, an electricallyconducting material may be provided on the DNA molecule. One example ofthe deposition of silver is described above. When depositing silver onthe DNA molecule that extends between the first electrode and the secondelectrode, no significant seeding and deposition of silver may takeplace on the R-loop, due to a lower density of silver ions.

The Ag⁺ ions form a salt with a phosphate ion in the DNA backbone. Inthe double helix, the O⁻ of the phosphate ions are evenly distributedaround the double helix. However, the density is about 50% lower in thestrand forming R-loop. Also, due to thermal vibration, as the Ag ion isreduced to Ag on the R-loop, it will migrate to the high density region,that is, the double helix region.

FIG. 6 illustrates an overhead view of an embodiment of the presentinvention after plating of an electrically conducting material 35 on aDNA molecule 21 extending between a first electrode 3 and a secondelectrode 5 by bonding to DNA molecules 17 and 19 attached to the firstelectrode and the second electrode. The DNA molecule includes one R-loop27 with a nanoparticle 29 bonded thereto with at least one nucleotide31. The structure shown in FIG. 6 results in a capacitive linkage 37between electrically conducting material 35 on the DNA molecule 21 andthe nanoparticle.

FIG. 7 illustrates a cross-sectional view of the embodiment illustratedin FIG. 6. As can be seen in FIG. 7, the structure illustrated thereinalso results in formation of a capacitive linkage 39 between thenanoparticle and the electrode 11, which may be considered a gateelectrode.

By manipulating the number of electrodes, DNA molecules extendingbetween electrodes, R-loops, nanoparticles, and/or interconnectionsamong the electrodes, nanoparticles, and/or electrically conductingmaterial arranged on the DNA molecules extending between electrodes,various types of devices may be created with structures according to thepresent invention. The conditions within the structures of the presentinvention may also be manipulated to create certain effects. Forexample, at a given bias, current in the electrically conductingmaterial on the DNA molecule that extends between the first electrodeand the second electrode may be controlled by regulating a charge in thenanoparticle. This may be done as in a typical Resonant Tunneling Devicereferred to above and described in detail by Seabaugh et al., referredto and incorporated by reference above.

Along these lines, FIG. 8 illustrates an embodiment of the presentinvention that includes two electrodes 41 and 43 similar to electrodes 3and 5 in the embodiment shown in FIGS. 1a-1 f. The embodiment depictedin FIG. 8 also includes an organic structure that includes at least oneDNA molecule 45 extending between electrodes 41 and 43. An electricallyconducting material 47 is arranged on the DNA molecule. The DNA moleculeincludes two R-loops 49 and 51, each including one nanoparticle 53 and55 bound thereto. Furthermore, the embodiment portrayed in FIG. 8includes two electrodes 57 and 59, similar to electrode 11 in theembodiment illustrated in FIGS. 1a-1 f, acting as gate electrodes,arranged under the R-loops 49 and 51 and the associated nanoparticles 53and 55. The structure illustrated in FIG. 8 may form an AND gate.

According to another alternative, the present invention could include astructure such as that illustrated in FIG. 9. FIG. 9 shows an embodimentof the present invention that basically includes two embodiments such asthe one shown in FIGS. 1a-1 f. Accordingly, the embodiment of thepresent invention depicted in FIG. 9 includes two pairs of electrodes 61and 63 and 65 and 67. The embodiment portrayed in FIG. 9 also includes apair of organic structures that each includes at least one DNA molecule69 and 71 extending between electrodes 61 and 63 and electrodes 65 and67, respectively. An electrically conducting material 73 and 75 isarranged on the DNA molecules 69 and 71, respectively. The DNA moleculeseach include one R-loop 77 and 79, each R-loop including onenanoparticle 81 and 83, respectively, bound thereto. Furthermore, theembodiment portrayed in FIG. 9 includes an electrode 85 and 87, similarto electrode 11 in the embodiment illustrated in FIGS. 1a-1 f, acting asgate electrodes, arranged under the R-loops 77 and 79 and the associatednanoparticles 81 and 83.

The structure illustrated in FIG. 9 may form an OR gate. This may beaccomplished by providing an electrical connection 89 between electrodes61 and 65, an electrical connection 91 between electrodes 63 and 67, andelectrical connections 93 and 95 to gate electrodes 85 and 87,respectively.

The foregoing description of the invention illustrates and describes thepresent invention. Additionally, the disclosure shows and describes onlythe preferred embodiments of the invention, but as aforementioned, it isto be understood that the invention is capable of use in various othercombinations, modifications, and environments and is capable of changesor modifications within the scope of the inventive concept as expressedherein, commensurate with the above teachings, and/or the skill orknowledge of the relevant art. The embodiments described hereinabove arefurther intended to explain best modes known of practicing the inventionand to enable others skilled in the art to utilize the invention insuch, or other, embodiments and with the various modifications requiredby the particular applications or uses of the invention. Accordingly,the description is not intended to limit the invention to the formdisclosed herein. Also, it is intended that the appended claims beconstrued to include alternative embodiments.

We claim:
 1. A structure, comprising: an electrode in electrical contactwith a biomolecule; an R-loop bound to said biomolecule; and ananoparticle bound to said R-loop.
 2. A structure, comprising: asubstrate; first and second electrodes on said substrate; bridging DNAextending between said first and second electrodes; at least one RNAstrand complementary to a region of said bridging DNA wherein said atleast one RNA strand and said DNA region bond to form at least oneR-loop; and a nanoparticle bonded to said DNA within said R-loop.
 3. Thestructure according to claim 2, wherein said electrodes are gold.
 4. Thestructure according to claim 2, wherein said DNA is double stranded. 5.The structure according to claim 2, wherein said DNA is λ-DNA.
 6. Thestructure according to claim 2, wherein at least one nucleotide isattached to said nanoparticle.
 7. The structure according to claim 6,wherein said at least one nucleotide is complementary to at least onenucleotide of said DNA molecule within said R-loop.
 8. The structureaccording to claim 6, wherein the at least one nucleotide iscomplementary to at least one nucleotide of the DNA molecule within theR-loop at a location equidistant from the first electrode and the secondelectrode.
 9. The structure according to claim 2, further comprising:first and second linker nucleic acid molecules respectively bonded to asurface of said first and second electrodes.
 10. The structure accordingto claim 9, wherein said first and second linker nucleic acids areselected from the group consisting of RNA and DNA.
 11. The structureaccording to claim 9, wherein said linker nucleic acid is sulfurterminated and single stranded.
 12. The structure according to claim 10,wherein said first linker nucleic acid has a different sequence thansaid second linker nucleic acid.
 13. The structure according to claim10, wherein each of said linker nucleic acids is from about five toabout 100 base pairs.
 14. The structure according to claim 10, whereinsaid bridging DNA comprises a first sticky end that hybridizes with saidfirst linker nucleic acid and a second sticky end that hybridizes withsaid second linker nucleic acid.
 15. The structure according to claim 2,further comprising: an electrically conducting material on said bridgingDNA.
 16. The structure according to claim 15, wherein the electricallyconducting material includes silver ions bonded to phosphate groups ofthe DNA molecule.
 17. The structure according to claim 15, wherein theelectrically conducting material includes metallic silver on the DNAmolecule.
 18. The structure according to claim 2, further comprising: athird electrode on the substrate between the first electrode and thesecond electrode.
 19. The structure according to claim 18, wherein thethird electrode is equidistant from the first electrode and the secondelectrode.
 20. The structure according to claim 18, wherein the thirdelectrode has a width of about 100 nm to about 5000 nm.
 21. Thestructure according to claim 18, wherein the third electrode has a widthof less than 100 nm.
 22. The structure according to claim 18, whereinthe third electrode is perpendicular to said bridging DNA.
 23. Thestructure according to claim 18, wherein said bridging DNA contacts saidthird electrode.
 24. The structure according to claim 2, wherein saidfirst and second electrodes are separated by a distance of about 1 μm toabout 100 μm.
 25. The structure according to claim 2, wherein the firstelectrode and the second electrode are made of a material that includesgold.
 26. The structure according to claim 2, wherein the firstelectrode and the second electrode are made of an oxide-free material.27. The structure according to claim 2, wherein the first electrode andthe second electrode terminate in sharp tips that face each other. 28.The structure according to claim 2, wherein the substrate is made of amaterial that includes a glass.
 29. The structure according to claim 18,further comprising: a fourth electrode positioned between the firstelectrode and the second electrode.
 30. The structure according to claim29, wherein the fourth electrode has a width of about 100 nm to about5000 nm.
 31. The structure according to claim 29, wherein the fourthelectrode has a width of less than 100 nm.
 32. The structure accordingto claim 29, wherein the fourth electrode is perpendicular to saidbridging DNA.
 33. The structure according to claim 29, wherein saidbridging DNA contacts the third electrode and the fourth electrode. 34.The structure according to claim 33, wherein the electrodes and saidbridging DNA form an AND gate.
 35. The structure according to claim 2,further comprising: a third electrode and a fourth electrode on thesubstrate; second bridging DNA molecule extending between the thirdelectrode and the fourth electrode; and a nanoparticle bonded to saidsecond bridging DNA.
 36. The structure according to claim 35 furthercomprising: a fifth electrode on the substrate arranged at least betweenthe first electrode and the second electrode; and a sixth electrode onthe substrate arranged at least between the third electrode and thefourth electrode.
 37. The structure according to claim 36, wherein: saidbridging DNA molecules contact the fifth electrode and the sixthelectrode; and the electrodes and the DNA molecules are electricallyconnected together to form an OR gate.
 38. The structure according toclaim 37, wherein one of the first electrode and the second electrode iselectrically connected to one of the third electrode and the fourthelectrode and the other of the first electrode and the second electrodeis electrically connected to the other of the third electrode and thefourth electrode.
 39. The structure according to claim 2, furthercomprising: a plurality of nanoparticles bonded to the bridging DNA. 40.A method for controlling a device that includes a substrate, a firstelectrode and a second electrode on the substrate, bridging DNAextending between the first electrode and the second electrode, at leastone RNA strand complementary to a region of said bridging DNA whereinsaid at least one RNA strand and said DNA region bond to form at leastone R-loop, a nanoparticle bonded to DNA within said R-loop, and anelectrically conducting material on the organic molecule, the methodcomprising the steps of: creating a bias in the electrically conductingmaterial; and regulating a charge in the nanoparticle to effect a changein the current in the electrically conducting material.